Fresh Install Has Wrong Layout

Question: Fresh Install Has Wrong Layout

9.4 years ago by

Chris Cole • 150

Chris Cole • 150 wrote:

Hi, I've been using the subversion version of Galaxy for a while, but now I want to update to the latest mercurial release. I installed it in a new location as per the wiki and set-up the SGE settings as per my previous install and all the tests pass. It launches fine, but when viewing the website the frames seem to be off-by-one. i.e., the 'Tools' frame is empty except for "This link may not be followed from within Galaxy.", the tools are in the middle window and the 'History' frame has general information. I can't see any errors in the paster.log file, so where can I look to sort out this error? Thanks, Chris

galaxy • 1.1k views

ADD COMMENT • link •

modified 9.4 years ago by Nate Coraor ♦ 3.2k • written 9.4 years ago by Chris Cole • 150

9.4 years ago by

Nate Coraor ♦ 3.2k

United States

Nate Coraor ♦ 3.2k wrote:

Hi Chris, It sounds like you maybe be running through a proxy, away from the server root, without the proxy-prefix option set in universe_wsgi.ini? If so, have a look at the documentation here: http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy#Apacheconfigur ationwithGalaxynotatthewebserverroot --nate

ADD COMMENT • link written 9.4 years ago by Nate Coraor ♦ 3.2k

Hi Nate, Nope. There's no proxy configured. The only things I changed in the HTTP config part of the universe_wsgi.ini are the host and the port. Cheers, Chris -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096

ADD REPLY • link written 9.4 years ago by Chris Cole • 150

Chris, Could you send us your universe_wsgi.ini? We haven't seen this happen without a proxy before. --nate

ADD REPLY • link written 9.4 years ago by Nate Coraor ♦ 3.2k

Nate, in the URL you just sent, are the "Apache configuration with Galaxy not at the web server root" and "External authentication and $REMOTE_USER" mutually exclusive? cheers, Erick 2009/7/3 Nate Coraor <nate@bx.psu.edu>

ADD REPLY • link written 9.4 years ago by Erick Antezana • 570

Not at all. Here's a sample configuration: <location galaxy=""> AuthType Basic AuthName Galaxy AuthUserFile /htpasswd Require valid-user </location> # Required to pass REMOTE_USER <proxy http:="" 127.0.0.1:8080=""> Order deny,allow Allow from all </proxy> RewriteEngine on RewriteCond %{IS_SUBREQ} ^false$ RewriteCond %{LA-U:REMOTE_USER} (.+) RewriteRule . - [E=RU:%1] RequestHeader set REMOTE_USER %{RU}e RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy(.*) http://127.0.0.1:8080$1 [P] --nate

ADD REPLY • link written 9.4 years ago by Nate Coraor ♦ 3.2k

Nate, thanks for the piece of code. It worked perfectly on my test server. However, when I tried to put it the production serve, whose apache makes use of VirtualServers in contrast to my test server, it didn't work :-( I am able to authenticate using my ldap login/password but then the web site shows just a blank page... there is no message in paster.log; however, the apache log says: [Tue Jul 07 09:35:29 2009] [error] PHP Warning: include(/apache/prod/html/php/menuLoader.php) [function.include]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error401.html on line 2 [Tue Jul 07 09:35:29 2009] [error] PHP Warning: include() [function.include]: Failed opening '/apache/prod/html/php/menuLoader.php' for inclusion (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error401.html on line 2 [Tue Jul 07 09:35:29 2009] [error] File does not exist: /apache/prod/html/galaxy [Tue Jul 07 09:35:29 2009] [error] PHP Warning: require_once(Menu.inc) [function.require-once]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error404.html on line 2 [Tue Jul 07 09:35:29 2009] [error] PHP Fatal error: require_once() [function.require]: Failed opening required 'Menu.inc' (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error404.html on line 2 [Tue Jul 07 09:35:29 2009] [error] File does not exist: /apache/prod/html/favicon.ico, referer: http://intranet/galaxy/ [Tue Jul 07 09:35:29 2009] [error] PHP Warning: require_once(Menu.inc) [function.require-once]: failed to open stream: No such file or directory in /apache/prod/html/ApacheErr/error404.html on line 2, referer: http://intranet/galaxy/ [Tue Jul 07 09:35:29 2009] [error] PHP Fatal error: require_once() [function.require]: Failed opening required 'Menu.inc' (include_path='.:/usr/share/pear:/usr/share/php') in /apache/prod/html/ApacheErr/error404.html on line 2, referer: http://intranet/galaxy/ Do you know what could be the problem? thanks, Erick 2009/7/3 Nate Coraor <nate@bx.psu.edu>

ADD REPLY • link written 9.4 years ago by Erick Antezana • 570

Any idea what's generating all the PHP errors? This is unrelated to Galaxy.

ADD REPLY • link written 9.4 years ago by Nate Coraor ♦ 3.2k

Hi Nate, yes, those PHP lines were just noise from the file... Anyway, we fixed the problem by removing the Virtual servers. SO everything is working fine. thanks Erick 2009/7/13 Nate Coraor <nate@bx.psu.edu>

ADD REPLY • link written 9.4 years ago by Erick Antezana • 570

Similar posts • Search »